NAMD 2.6b1 includes a new option vdwGeometricSigma that provides the proper Lennard-Jones parameter combining rule for the OPLS force field.

The parameters are apparently available via a link from http://brooks.chem.lsa.umich.edu/charmm_docs/charmm.htm to http://brooks.chem.lsa.umich.edu/charmm_docs/Data/oplsaa-toppar.tgz

(old: http://brooks.scripps.edu/charmm_docs/charmm.htm to http://brooks.scripps.edu/charmm_docs/Data/oplsaa-toppar.tgz)

NOTE: (quoting from the README file of the above mentioned tar): "The topology and parameter files here include only the protein portion of the OPLS-AA force field. User-defined topology and parameter files are required for other functionalities."